The F-35 Joint Strike Fighter program is flying into this year’s budget wars on Capitol Hill with renewed lift under its wings from a lower government cost estimate and progress refining technical glitches.

Another boost for the long-delayed and over budget program — testimonials by pilots who say its flight control systems could usher in a new era of naval aviation, one in which landing by night on ships is a breeze, freeing training dollars and time.

But the Government Accountability Office warned in two recent reports that delays in development of critical software in the radar-evading aircraft are threatening the target date of July 2015 to declare it ready for combat.

The F-35 is the most costly and ambitious acquisition program in Pentagon history. Prime contractors Lockheed Martin and engine-maker Pratt and Whitney are developing three versions of the stealthy strike fighter for the U.S. military, as well as eight international partners. The Marines plan to replace their F/A-18 Hornets and AV-8B Harriers with the vertically landing F-35B. The Navy wants the tailhooking carrier version to supplement its Super Hornets. And the Air Force will fly a conventional model with its tactical fleet.

The GAO announced last week in its annual U.S. arms report that the F-35 would cost $11.5 billion less in fiscal 2014 dollars compared to the previous year, or an estimated $332.3 billion for 2,457 aircraft.

Adding the cost to sustain and operate the aircraft puts the price for the F-35 program at more than $1 trillion, a sum the Defense Department says is too high. The Pentagon has invested about $35 billion so far to procure 150 aircraft through 2013. An average of about $12.6 billion annually through 2037 is needed.

“To execute the program as planned, the Department of Defense will have to increase funds steeply over the next five years,” the GAO told Congress. “Annual funding of this magnitude clearly poses long-term affordability risks given the current fiscal environment.”

When the program began in 2001, each jet was estimated to cost about $78 million. Including a 14 percent reduction in the number of aircraft, the unit cost now is nearly double that at $135 million.

The lower GAO cost estimate was shot down by Winslow Wheeler, of the Project On Government Oversight. Wheeler, a vocal critic of the F-35 program and a former GAO worker, said in an online report for the watchdog group that what was billed as savings from greater “efficiencies” was really a regurgitation of outdated Pentagon reports based on “rejiggering inflation numbers, lesser hardware requirements, and unverified subcontractor numbers.”

Design problems and revisions during testing and development are continuing to add to the bottom line. Chief among them have been problems with jitter, poor night vision acuity and light leakage in the helmet mounted display.

Bulkhead and rib cracks were discovered last year in the Marines’ F-35B version. And the carrier version set to begin ship trials in October had to be modified to help it catch the wire.